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R
Bash
Python
Web Development
SQL
C++

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Source code available at github.com/sruizcarmona/,
built with datadrivencv package

Last updated on May 21, 2021

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Sergio Ruiz-Carmona

I am currently a Research Officer and Bioinformatician at the Baker Institute, under the supervision of professor Mike Inouye. My research interests are broad and involve mainly the relationship between genetic variants and their effect on protein structures.

I carried out my MSc and PhD in Barcelona in the Barril Lab, where I worked with different structure-based drug design methods with the aim to improve drug design for non-standard targets.

Education

PhD in Biomedicine

Universitat de Barcelona

Barcelona, ES

2017 - 2012

  • Virtual Screening for novel MoA: Apps. and method developments
  • Development and application of structure-based drug discovery methods
  • Awards: Extraordinary prize for PhD Thesis and Ramon Margalef award for best publication

MSc in Bioinformatics for Health Sciences

Universitat Pompeu Fabra

Barcelona, ES

2012 - 2010

  • Expanding Druggable Genome: PP-Interfaces as a new target class
  • Study of novel rational approach to find PP interfacial binders

BSc in Biotechnology

Universitat Autònoma de Barcelona

Barcelona, ES

2010 - 2006

Research Experience

Research Officer and Bioinformatician

Inouye Lab
Baker Heart and Diabetes Institute

Melbourne, AU

Today - 2019

  • I am working in a project that overlaps Structural Biology and Genomics, in collaboration with David Ascher’s Lab. Mainly, I am trying to understand how rare missense variants alter protein structures and can induce disease
  • My role also involves giving Bioinformatics support to the whole institute, where I apply different statistical and data analysis methods in a wide range of projects, mainly related with cardiovascular diseases and diabetes

Postdoctoral Researcher

Barril Lab, Universitat de Barcelona

Barcelona, ES

2018 - 2017

  • After finishing my PhD, I worked in exciting collaborative projects in the field of epigenetics and cancer, where I carried out multidisciplinary research and learned new experimental skills

EMBO Short-Term Fellow

Andreas Bender Lab, Unversity of Cambridge

Cambridge, GB

2017

  • I spent 2 months in one of the main Pharmacogenomics groups in the world, where I used gene-expression profiles of different biological systems to study BRD4 and drug selectivity
  • 2 months (Sep/Oct 2017) research stay. Funded by EMBO (also awarded FEBS Short-Term Fellowship)

MuTaLig COST Action Short-Term Fellow

Peter Kolb Lab, Philipps Universität Marburg

Marburg, DE

2017

  • I applied the methods developed during my PhD, Dynamic Undocking, Docking and MD simulations, in order to find multipotent compounds targeting RNAse P of extremely pathogenic bacteria
  • 1 month (Nov 2017) research stay. Funded by MuTaLig COST Action

Predoctoral Researcher

Barril Lab, Universitat de Barcelona

Barcelona, ES

2016 - 2011

  • Master’s and PhD research projects in the Xavier Barril Lab
  • I applied a combination of experimental and computational techniques to study non-standard drug targets. I also developed novel structure-based computational methods to help in identifying novel drugs

I have been working in several multidisciplinary research groups around the globe. I have applied a broad range of concepts and ideas in the drug discovery field (both experimental and computational) and also in genomics and data analysis

Skills and Training

Computational Techniques

Computer-Aided Drug Discovery (SBDD), Virtual Screening, Docking, Molecular Dynamics, Chemoinformatics, Quantum Chemistry, Bioinformatics Tools and Analysis

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Scientific Software

Bioinformatics software, pymol, openbabel, databases, molecular docking programmes and molecular modelling tools (Schrödinger, MOE)

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Programming

R, Python, Perl, C++, LaTeX, Bash, Java, MySQL, HTML and Android and Web Development

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Experimental Techniques

Biophysical Screening (SPR, DSF), Cell Growth, Protein Expression and Purification

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Selected Publications

I collaborated with different companies (Servier, Repsol and Vernalis) where I studied physicochemical properties of both small molecules and drug targets and also developed novel methods for virtual screening

Oxygen Pathway Limitations in Patients with Chronic Thromboembolic Pulmonary Hypertension

Circulation
Read it here

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2021

  • Erin J Howden *, Sergio Ruiz-Carmona *, […] Andre La Gerche, Marion Delcroix and Guido Claessen

Dynamic Undocking: A Novel Method for Structure-Based Drug Discovery

Rational Drug Design (Book Chapter)
Read it here

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2018

  • Maciej Majewski, Sergio Ruiz-Carmona and Xavier Barril

Dynamic undocking and the quasi-bound state as tools for drug discovery

Nature Chemistry
Read it here

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2017

  • Sergio Ruiz-Carmona, P Schmidtke, […] Rod Hubbard and Xavier Barril
  • Highlighted in its issue cover

Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR

Journal of Computer-Aided Molecular Design
Read it here

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2017

  • Y Westermaier, Sergio Ruiz-Carmona, […] Pierre Ducrot and X Barril

rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids

PLoS Computational Biology
Read it here

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2014

  • Sergio Ruiz-Carmona, Daniel Alvarez-Garcia, […] Xavier Barril, Rod Hubbard and S David Morley

I consider myself a passionate teacher. I have always volunteered and enrolled in as many teaching opportunities as possible during the different stages of my career

Teaching Experience

Introduction to R Course

Introduction to Stats Analyses Using R

Melbourne, AUS

2021

  • 6h of online tutoring for Baker Heart and Diabetes Institute researchers
  • Organized by Prof. Agus Salim and Dr. Gad Abraham

Associate Professor

Faculty of Pharmacy, Universitat de Barcelona

Barcelona, ES

2019 - 2015

  • Classes in Pharmacy, Food Science and Nutrition degrees (total 400h)

Molecular Dynamics workshops

Novel methods for Drug Discovery

Marburg, DE

2017

  • 6h theory and hands-on workshop for Dynamic Undocking and MDmix simulations. During my research visit at Kolb’s Lab

Drug Discovery workshop

Computer-aided Drug Design

Ciudad de Mexico, MX

2016

  • Organized and imparted 30h of theory and hands-on sessions for researchers at the Instituto de Química (Chemistry Institute), at the UNAM
  • With Profs. Xavier Barril and Axel Bidon-Chanal

Scientific Communications

I have also developed rDock and Barril Lab websites, used as dissemination platforms where the different tutorials and blog entries are shared with the community

Characterization of the effect of disease-causing genetic variants using protein 3D structural alterations

Lorne Proteins 2021
Virtual Poster Presentation

Lorne, AUS

2021

Var2Prot: A new tool to unravel the 3D structural effect of genetic variants

Lorne Proteins 2020
Oral Communication

Lorne, AUS

2020

Var2Prot: A new tool to unravel the 3D structural effect of genetic variants

GIW/ABACBS 2019
Poster Presentation

Sydney, AUS

2019

New approaches in SBDD: Applications to non-standard targets

Joint Klebe & Kolb Seminars
Invited Oral Communication

Marburg, DE

2017

Virtual Screening for novel mechanisms of action: Applications and method developments

Andreas Bender Lab Seminars
Invited Oral Communication

Cambridge, UK

2017

Dynamic Undocking and the Quasi-Bound State as Tools for Drug Discovery

7th Joint Sheffield Conference on Chemoinformatics
Oral Communication

Sheffield, UK

2016

Dynamic Undocking and the Quasi-Bound State as Tools for Drug Discovery

III Symposium of Young Researchers in Medicinal Chemistry
Oral Communication

Barcelona, ES

2016

Dynamic undocking of protein complexes: a new tool for ligand discovery

Gordon Research Conference: New Frontiers in CADD
Poster Presentation

Mount Snow (VT), USA

2015

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

8th International Workshop on New Approaches in Drug Design
Poster Presentation

Marburg, DE

2014

Data Science Writing

rDock Docking Manuals and Tutorials

rDock website content

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2015 - 2012

  • I developed and validated different tutorials for using rDock, with around 300 visits every month

Small Molecule Parametrization

Blog entry

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2013

  • Blog entry about how to parametrize small molecules using Gaussian and AMBER forcefield, for Molecular Dynamic simulations
  • 50 reads per month

Selected Press Stories

Australasian Leadership Computing Grants

Story about NCI Computing Grant

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2021 - 2020

  • Together with Mike Inouye, we were awarded a 1 year computing grant by the Australian National Compuational Infrastructure to study COVID-19 proteins and possible drug treatments

Dynamic Undocking paper publication

News about our publication and selection for cover

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2017

  • Highlight from Universitat de Barcelona about our Dynamic Undocking publication in Nature Chemistry and its selection for the March 2017 printed cover